I'm only going to ever main the character I enjoy playing as the most. To me, gameplay is always the only thing when choosing who to play.
Whoever makes me the most hyped to play is who I play as.
In 64 that's Mario (Falcon ain't too far behind), in Melee that's Fox (although Marth is close), in Brawl that was Toon Link, in Project M it's a mess (I'm always torn between Marth, Roy, Fox, and Ness), and in Smash 4 right now it's Toon Link again (although Lucina is close).
The only time I would suggest to ever switch a main is if they are so terrible that they are limited and those limits make them boring. Kirby in Melee did that for me, and I figured that out within a few months.
However, in MvC2, tiers are a super big deal and there's a big difference (ignoring the tier tweener characters who are in between "true" tier categories) between the 4 Gods, the high tiers, the mid-tiers, the low tiers, the bottom tiers, and Roll. I actually in that game almost exclusively play mid-tier characters because I enjoy mid-tier play the most. There's no infinite combos, no broken stuff, and the defense feels super smooth. Plus characters like Mega Man, Spider-Man, and Wolverine have designs in that game I just absolutely LOVE TO DEATH!!!!
So if you enjoy mid, low, bottom tier play over all tier play (mostly high and top tier), there's nothing wrong with that either. There's always a crowd in fighting games that prefer that over the top tiers.
Just be aware of what kind of style of gameplay, character, game direction, and game balance you like the most, and embrace it.